Dexter is caught up in a very personal case that once again awakens the needs of his Dark Passenger; Debra feels overwhelmed by her new Lieutenant duties, made all the more complicated when she finds out Quinn slept with a witness in the Doomsday case.
Dexter gets a call from Debra telling him she needs to see him about something urgent. Back at the station, Debra says that "The Trinity Killer" has killed again, the latest victims being his own wife, Sally, who was bludgeoned to death with a hockey stick and his daughter, Rebecca, who was killed in a similar manner to the bathtub murders. Jonah was the only survivor from the attack. Debra doesn't know that Dexter had killed the real "Trinity." To Dexter, Jonah seems to be the likely suspect. Dexter tells Debra that he needs some time since this happened right after Brother Sam's death. She agrees to a day.
Travis Marshall tells his sister, Lisa Marshall, that he is taking time off from his job. Travis notices Professor James Gellar outside the house. He tells Gellar that he's "done" but Gellar orders Travis to finish carrying out God's work.
Brian and Dexter think that Jonah, the son of a serial killer, is following in his father's footsteps. Brian goads Dexter to drive the thirty hours to Kearney, Nebraska, and kill Jonah. When Dexter hesitates, Brian tells him that he has been domesticated and he needs to have fun. Dexter decides he will go. He asks Jamie Batista to stay at his place and take care of Harrison for several days. While on the road, Dexter calls Debra to inform her that he will need more than one day off. She isn't happy as she needs his help with the Doomsday Killer Case.
Maria LaGuerta embarrasses Debra during her presentation of ComStat figures. Debra confronts her in the elevator about it, and Maria says that, because she is now Captain, the figures reflect on her.
When Dexter stops at a convenience store, he notices a revolver behind the counter. He distracts the young clerk by flirting with her, and then having sex with her in a back room. While she is getting dressed afterward, he steals the gun on his way out. With Brian urging him on, Dexter laughs, begins to drive faster, and shoots at road signs out of the car window until the gun is empty.
Dexter locates Jonah at his place of work, a hardware store. Jonah greets Dexter with, "Hello, Dexter Morgan." These are the same words said by Arthur Mitchell when he discovered Dexter's true identity. In a subsequent conversation, Jonah tells Dexter that he saw his father kill his mother. Dexter knows this a lie since he had killed Arthur Mitchell. Jonah tells Dexter to go back to Miami. Brian tells Dexter the fun has just begun.
Debra and Angel interview Holly Benson, a woman set free by Travis. Holly says that she had been blindfolded, forced to drink blood, and called "The Whore."
Dexter pays cash to a suspicious guy, Norm, for a motel room. Norm notices Dexter's Florida plates and questions him on why he is in the area. Dexter makes up a story about being a landscaper and following the Oregon Trail. He asks Norm where he can get a flat tire fixed, and Norm offers to plug it for twenty dollars. When Norm mentions that Dexter has soft hands for a landscaper, Dexter smirks and says that he wears gloves.
As he takes a shortcut through a cornfield while walking into town, Dexter finds a small pot farm. Norm, who is watching Dexter from afar, realizes that Dexter has discovered his secret.
Deb's team determine that Professor Gellar's young assistant is likely one of his former students. Louis, using his software, narrows the list of possible student assistants to 200. Travis is one of them.
Louis shows Jamie a video game that he is creating based on police cases. An upset Debra drops by, and asks Jamie where Dexter went on his trip. She says, maybe, the Keys.
Because Dexter won't answer her calls, Debra tries from his home number. Dexter picks up, thinking it is Jamie. He doesn't give Debra any information, and hangs up. He decides to deal with Jonah right away.
Norm finishes the tire and Dexter drives to Jonah's house. Dexter is still not sure if Jonah's guilty, which disgusts Brian. When Dexter opens his trunk, he sees that his knives and forensic kit are missing. He believes that Norm took them. Jonah's house is unlocked and Dexter enters to look around. While running a test for bleach, Jonah arrives home. He is very angry to see Dexter there and orders him go get out or he will call the police. Dexter tells Jonah that Trinity was never in the house, because he had killed him. Jonah runs out of the house and takes off in his car.
Dexter returns to the motel to get his knives back from Norm. Dexter finds Norm in a shed. Norm tries to extort $10,000 from Dexter for his own knives. Dexter refuses and attempts to grab his knives. Norm pulls out the gun he found in Dexter's car and threatens to kill Dexter. However, Dexter knows the gun is unloaded and impales Norm with a pitchfork. Brian tries to convince Dexter that it doesn't matter if a victim is guilty or not. Dexter seemingly likes the idea of continuing to kill, unrestrained by The Code. With no ocean nearby, Dexter disposes of Norm's body in a nearby grain silo.
Travis returns Gellar's things to him, and states again that he is done. Gellar begins to list the sins that people commit. Travis says that he wants to be free. Gellar replies, "Talk to God, I release you."
Quinn apologizes to Deb for proposing marriage. He said he thought it was "something people did." He kisses her on the cheek, but Debra reminds him that it is over.
Jonah calls Dexter and arranges a private meeting in his hardware store. Jonah immediately attacks Dexter, but he is quickly subdued. With a knife to his throat, Jonah asks Dexter to kill him, which puzzles Dexter. Jonah explains that his sister committed suicide, due to abuse by their mother, who had blamed them for Arthur's actions. When Jonah found his sister dead, he exploded with anger and killed his mother. He shows remorse.
Despite Brian egging him on to kill Jonah, Dexter realizes that Jonah has a conscious and lets him live. Dexter pushes past Brian and gets in his car. He tells Jonah to forgive himself. He then runs his car into Brian, which causes Brian's illusion to dissipate. As Dexter nears Miami, he stops to pick up Harry, who is standing on the side of the road.